Example Notebooks for 001259

001259/README.md

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+# Example Sessions for Dandiset 001259
+
+This submission provides 2 notebooks showcasing example sessions for the Dandiset 001259.
+
+Each notebook provides an example of how to access the critical data and metadata from the 2 types of experiments in the dataset:
+
+- `ephys_example_notebook.ipynb` showcases one example session from the 001259 dataset containing operant behavior and concurrent OpenEphys recordings in primary auditory cortex (A1).
+- `optogenetics_example_notebook.ipynb` showcases one example session from the 001259 dataset containing operant behavior and concurrent optogenetic stimulation.

001259/environment.yml

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+# run: conda env create --file environment.yml
+name: schneider_notebook_env
+channels:
+    - conda-forge
+dependencies:
+    - python==3.12
+    - ipykernel
+    - matplotlib
+    - dandi
+    - pip
+    - pip:
+      - remfile
+      - schneider-lab-to-nwb @ git+https://github.com/catalystneuro/schneider-lab-to-nwb.git@main

001259/stream_nwbfile.py

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+from pynwb import NWBHDF5IO
+import remfile
+import h5py
+from dandi.dandiapi import DandiAPIClient
+
+def stream_nwbfile(DANDISET_ID, file_path):
+    '''Stream NWB file from DANDI archive.
+
+    Parameters
+    ----------
+    DANDISET_ID : str
+        Dandiset ID
+    file_path : str
+        Path to NWB file in DANDI archive
+
+    Returns
+    -------
+    nwbfile : NWBFile
+        NWB file
+    io : NWBHDF5IO
+        NWB IO object (for closing)
+
+    Notes
+    -----
+    The io object must be closed after use.
+    '''
+    with DandiAPIClient() as client:
+        client.dandi_authenticate()
+        asset = client.get_dandiset(DANDISET_ID, 'draft').get_asset_by_path(file_path)
+        s3_url = asset.get_content_url(follow_redirects=1, strip_query=False)
+    file_system = remfile.File(s3_url)
+    file = h5py.File(file_system, mode="r")
+    io = NWBHDF5IO(file=file, load_namespaces=True)
+    nwbfile = io.read()
+    return nwbfile, io